6-426155-G-T

Variant names:

• chr6-426155-G-T
• rs9378815

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0237 in 152,226 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (56 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (3611/152226) while in subpopulation NFE AF= 0.0328 (2233/68006). AF 95% confidence interval is 0.0317. There are 56 homozygotes in gnomad4. There are 1707 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3615 AN: 152106 Hom.: 56 Cov.: 34

Gnomad AFR AF: 0.00763

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00931

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0328

Gnomad OTH AF: 0.0321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0237 AC: 3611 AN: 152226 Hom.: 56 Cov.: 34 AF XY: 0.0229 AC XY: 1707 AN XY: 74428

Gnomad4 AFR AF: 0.00764

Gnomad4 AMR AF: 0.0286

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00911

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0328

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.00921 Hom.: 917

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.20
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9378815; hg19: chr6-426155;